rs659527

Variant names:

• chr9-32527326-A-G
• rs659527
• ENST00000681750.1:c.-45+23448T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-32527326-A-G
• chr9-32527326-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681750.1(ENSG00000288684):​c.-45+23448T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,826 control chromosomes in the GnomAD database, including 28,737 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (28737 hom., cov: 30)
• Consequence: ENSG00000288684 ENST00000681750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 8 publications found

Genes affected

ENSG00000288684 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288684	ENST00000681750.1	c.-45+23448T>C		intron_variant	Intron 3 of 19			ENSP00000506413.1
ENSG00000288684	ENST00000680198.1	n.198+23448T>C		intron_variant	Intron 2 of 18			ENSP00000505143.1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93045 AN: 151708 Hom.: 28704 Cov.: 30

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93117 AN: 151826 Hom.: 28737 Cov.: 30 AF XY: 0.607 AC XY: 45010 AN XY: 74186

African (AFR) AF: 0.658 AC: 27216 AN: 41358

American (AMR) AF: 0.527 AC: 8047 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2133 AN: 5162

South Asian (SAS) AF: 0.638 AC: 3077 AN: 4824

European-Finnish (FIN) AF: 0.516 AC: 5413 AN: 10496

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.633 AC: 42976 AN: 67946

Other (OTH) AF: 0.603 AC: 1263 AN: 2094

Alfa AF: 0.630 Hom.: 14985

Bravo AF: 0.611

Asia WGS AF: 0.523 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.90
PhyloP100		-0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs659527; hg19: chr9-32527324;